Since 1991, the French Ministry of Culture and Communication has undertaken a vast restoration campaign of Villa Medici involving the ensemble of constructions on the estate as well as the gardens, in order to re-establish the splendor of this late XVIth century Renaissance palace. Works began in 1991 with the restoration of the Galerie du Bosco, an extension of the library wing whose façade had been eroded by humidity. Works continued between 1994 and 1997 with the restoration of the façade of the Villa giving onto the piazzale. This unique façade is often cited as one of the most magnificent presentations of antiquarian collections in the Renaissance. In depth studies on the state of conservation lasting over a year demonstrated that the original construction materials were in a satisfactory state to the relief and joy of all and sundry. The restoration of the courtyard and its covering (façades and roofing) of the Villa were terminated in 2000.

In 2001, after the appearance of disquieting cracks, a study on the structural solidity of the Villa was launched. The conclusions were alarming: the resistance values of the materials of the partition walls were comparable to those of sand. The Italian authorities and the French General Inspector of Historical Monuments quickly came to an agreement on the financial and labour necessities for the consolidation of the structures of Villa Medici. The works, which began at the ground floor and proceeded to the upper floors, recovered the entirety of the partition walls by following a very specific innovative technique. Prestressed steel tension bars between two anchor plates traversed the walls from side to side, the ensemble was unified with bands of carbon fiber applied horizontally to the walls. From 2007, the restoration project resumed parallel to the works of consolidation with the renewed waterproofing of the vaulting of the antique cistern, the cleansing of the loggia, as well as of the inside construction sites for the restauration of the three rooms belonging to the Cardinal terminated in 2012. The painted caissoned ceilings and the frescoed friezes realized by Jacopo Zucchi and the murals in the apartment of the Director were restored in the same period of time.

The 8 hectares of garden have also been undergoing restoration since 2001. These works concern not only the vegetation, but also the architectural elements: the restoration of the Parnasse with the replacing of the fountain in its original position, (2002-2005), the recovery of the Loggia of Cleopatra, (2009-2010), that of the statuary, the fountains (six of which were restored between 2006 and 2007) as well as various monumental gateways (the Vignola portal in 2007, the San Vittorio portal in 2012). Finally, always in the garden, the Ferdinando de Medici pavilion was the object of an exemplary restoration in 2011 returning the éclat to the frescoes of the aviary realized by Jacopo Zucchi in 1576 – 1577, and which were recovered by fellow of the Academy Géraldine Albers in 1985. The actions on the vegetation began in 2003 with the definition of the geometric scheme by repositioning the hedges surrounding the sixteen squares in the historical garden as well as the herms which mark the corners. The parterre was replanted according to a XIXth century design in 2005. More specific actions in the squares consist of the creation of a vegetable garden and an orchard. Since 2010, particular attention has been devoted to the eco-responsible management of the garden and the conservation of the arboreal legacy of the park.